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- PDB-2qcz: Structure of N-terminal domain of E. Coli YaeT -

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Basic information

Entry
Database: PDB / ID: 2qcz
TitleStructure of N-terminal domain of E. Coli YaeT
ComponentsOuter membrane protein assembly factor yaeT
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / POTRA domain
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / cell adhesion / membrane
Similarity search - Function
membrane protein fhac / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) ...membrane protein fhac / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKim, S. / Malinverni, J.C. / Sliz, P. / Silhavy, T.J. / Harrison, S.C. / Kahne, D.
CitationJournal: Science / Year: 2007
Title: Structure and function of an essential component of the outer membrane protein assembly machine.
Authors: Kim, S. / Malinverni, J.C. / Sliz, P. / Silhavy, T.J. / Harrison, S.C. / Kahne, D.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor yaeT
B: Outer membrane protein assembly factor yaeT


Theoretical massNumber of molelcules
Total (without water)74,9102
Polymers74,9102
Non-polymers00
Water0
1
A: Outer membrane protein assembly factor yaeT


Theoretical massNumber of molelcules
Total (without water)37,4551
Polymers37,4551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein assembly factor yaeT


Theoretical massNumber of molelcules
Total (without water)37,4551
Polymers37,4551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.721, 94.048, 109.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane protein assembly factor yaeT / Omp85


Mass: 37455.168 Da / Num. of mol.: 2 / Fragment: residues 21-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: yaeT / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A940

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 10% PEG 10K, 100mM sodium acetate, 100 mM magnesium formate, 10%glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97933, 0.97944, 0.97856
SYNCHROTRONAPS 19-ID20.97933
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979331
20.979441
30.978561
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
9.117.21392280.1031.0331524599.2
9.428.11297060.0931.123.11383299.3
9.236.91277920.1060.973.11389999.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465097.510.0541.4339.2
5.136.4698.710.0851.2759.2
4.485.1398.910.0771.1389.3
4.074.4899.510.0921.2259.5
3.784.0799.710.1211.0879.6
3.563.7899.710.1570.9389.6
3.383.5699.810.2120.8519.6
3.233.3899.910.3090.7989.5
3.113.2399.910.4510.7448.8
33.1198.410.6020.6987.1
6.675097.220.0441.19.1
5.36.6798.820.0811.2769.2
4.635.398.920.0711.1859.2
4.214.6399.320.0841.2849.4
3.914.2199.620.1041.3229.6
3.683.9199.720.1351.1419.6
3.493.6899.720.1731.0389.6
3.343.4999.920.2420.9729.6
3.213.3499.920.3510.9329.5
3.13.2199.720.490.8798.8
6.675097.230.0390.7919.1
5.36.6798.730.081.0039.2
4.635.398.830.0740.9989.3
4.214.6399.330.0941.1159.4
3.914.2199.630.1191.1449.5
3.683.9199.830.1641.0099.6
3.493.6899.730.2160.9459.6
3.343.4999.930.3090.9069.5
3.213.3499.930.4410.8839
3.13.2199.730.5910.8437.6
ReflectionResolution: 2.7→50 Å / Num. all: 20509 / Num. obs: 20418 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 32.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.84 / Num. unique all: 1960 / % possible all: 97.3

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Phasing

Phasing dmFOM : 0.55 / FOM acentric: 0.55 / FOM centric: 0.56 / Reflection: 20363 / Reflection acentric: 17823 / Reflection centric: 2540
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-47.2120.940.960.88946663283
4.8-7.70.870.90.7428002308492
3.9-4.80.840.850.7234572989468
3.4-3.90.680.70.5934273047380
2.9-3.40.370.370.3361005490610
2.7-2.90.130.130.1436333326307

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→50 Å / FOM work R set: 0.706 / Cross valid method: free R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 989 4.8 %RANDOM
Rwork0.263 ---
all0.308 20616 --
obs-20363 98.8 %-
Solvent computationBsol: 33.334 Å2
Displacement parametersBiso mean: 63.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.634 Å20 Å20 Å2
2---21.686 Å20 Å2
3---21.052 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 0 0 4834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3841.5
X-RAY DIFFRACTIONc_scbond_it1.9522
X-RAY DIFFRACTIONc_mcangle_it2.3982
X-RAY DIFFRACTIONc_scangle_it3.0982.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.750.508390.477832871
2.75-2.80.462560.4329941050
2.8-2.860.429580.3899951053
2.86-2.920.531570.37310001057
2.92-2.990.365380.37610181056
2.99-3.060.422510.34910341085
3.06-3.150.476580.34510141072
3.15-3.240.416490.3410171066
3.24-3.340.327390.28210381077
3.34-3.460.368600.28410121072
3.46-3.60.346420.27110351077
3.6-3.770.383580.2810131071
3.77-3.960.358450.2410451090
3.96-4.210.274420.22310401082
4.21-4.540.24570.20910261083
4.54-4.990.274560.2110501106
4.99-5.720.296630.24610331096
5.72-7.20.266670.24310691136
7.2-500.314540.23511091163
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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